Differential transcript usage StageR error message
Dear All,
I have used the recent protocol for DTU analysis from this recent version
I am facing some issues while doing the stagewise analysis for dtu
stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation, pScreenAdjusted=TRUE, tx2gene=tx2gene)
stageRObj <- stageWiseAdjustment(object=stageRObj, method="dtu", alpha=0.05)
Error in .stageWiseTest(pScreen = pScreen, pConfirmation = pConfirmation, :
NA p-values found in either the screening or confirmation tests.
If you want to allow for NA p-values, set allowNA = TRUE.
If I give allowNA = TRUE it is showing like this:
stageRObj <- stageWiseAdjustment(object=stageRObj, method="dtu", alpha=0.05, allowNA=TRUE)
Removing 4 features with NA screening hypothesis p-values.
Error in pConfirmation[id, ] : incorrect number of dimensions
Help me
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akilabioinfo •
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It is something to do with dimension of your input datasets, check
dim(pScreen),dim(pConfirmation), check the example datasets dimensions. Ensurestr()of your data is same as example datasets, etc. Joys of debugging.